1 Overview

Data

Normalization

Model options

Network processing

cor/cov method: pearson

2 Load and normalize data

Data

Normalization

2.1 Load TCGA data

See prepare.tcga.survival.data function for how to configure parameters.

This uses data packages from obtained from ‘github:averissimo/tcga’ that contain FPKM expression levels.

prepare.tcga.survival.data('skcm.data.2018.09.11',
                           'metastatic',
                            normalization        = 'center',
                            log2.pre.normalize   = TRUE,
                            handle.duplicates    = 'keep_first',
                            coding.genes         = TRUE,
                            subtract.surv.column = 'days_to_submitted_specimen_dx')

2.1.1 Summary of data

## [INFO]        Loaded data from TCGA: skcm.data.2018.09.11
## [INFO]               type of tissue: metastatic
## [INFO]   observations (individuals): 351 (174 event / 177 censored)
## [INFO]            variables (genes): 19844

2.1.2 Survival curve

2.2 Load degree data

Network processing

  • Degree calculation: string
  • Edge cutoff: 0
  • Unweighted edges

cor/cov method: pearson

  • only applies if network type is correlation/covariance

2.3 Preparing degree vector

  • Normalize degree between 0 and 1
  • Hub: heuristic( 1 - degree )
  • Orphan: heuristic( degree )
  • trans.fun is a double power to scale the values

see ?glmSparseNet::heuristicScale or ?glmSparseNet::hubHeuristic

# see ?glmSparseNet::heuristic.scale
trans.fun <- function(x) {
    heuristicScale(x) + 0.2
}

2.3.1 Genes with degree above 4000

ensembl_gene_id degree external_gene_name
ENSG00000150991 10394 ENSG00000150991
ENSG00000170325 6346 ENSG00000170325
ENSG00000100300 5797 ENSG00000100300
ENSG00000174775 5614 ENSG00000174775
ENSG00000142208 5573 ENSG00000142208
ENSG00000111640 5363 ENSG00000111640
ENSG00000163631 5260 ENSG00000163631
ENSG00000177606 4952 ENSG00000177606
ENSG00000141510 4936 ENSG00000141510
ENSG00000197122 4903 ENSG00000197122
ENSG00000254647 4592 ENSG00000254647
ENSG00000112062 4187 ENSG00000112062
ENSG00000170315 4114 ENSG00000170315
ENSG00000170345 4010 ENSG00000170345

2.3.2 Original degree frequency

Original

LOG10 Scale on X-axis

3 Model Inference

3.1 Train and test sets

## [INFO] Size of sets: (size/events)
##  * Train: 80.00% ::  280 /  139
##  *  Test: 20.00% ::   71 /  35
## [INFO] Number of variables per model:
Model BaseModel Alpha TargetVars nvars
Elastic Net Elastic Net 0.10 116 116
Hub Elastic Net 0.10 116 116
Orphan Elastic Net 0.10 116 116
Elastic Net Hub 0.10 41 41
Hub Hub 0.10 41 43
Orphan Hub 0.10 41 42
Elastic Net Orphan 0.10 111 116
Hub Orphan 0.10 111 113
Orphan Orphan 0.10 111 116 
## [INFO] note, selected variables could be slightly different from target, to have more accuracy increase nlambda in code

4 Results

4.1 Relative risk distribution

Calculated using the inferred models and the train/test datasets. The higher the better.

Test Set

Train Set

4.2 Kaplan-Meier Curves

4.2.1 Models on test sets

Elastic Net (base model: Elastic Net)

Test set

Training set

Hub (base model: Elastic Net)

Test set

Training set

Orphan (base model: Elastic Net)

Test set

Training set

Elastic Net (base model: Hub)

Test set

Training set

Hub (base model: Hub)

Test set

Training set

Orphan (base model: Hub)

Test set

Training set

Elastic Net (base model: Orphan)

Test set

Training set

Hub (base model: Orphan)

Test set

Training set

Orphan (base model: Orphan)

Test set

Training set

4.3 Summary Table

weighted penalization project tissue cutoff coding.genes alpha model nvars km.train km.test c.index.train c.index.test
FALSE string skcm.data.2018.09.11 metastatic 0 TRUE 0.10 Elastic Net 116 0 0.0220258 0.7563888 0.7043236
FALSE string skcm.data.2018.09.11 metastatic 0 TRUE 0.10 Hub 116 0 0.0298483 0.7752908 0.6799163
FALSE string skcm.data.2018.09.11 metastatic 0 TRUE 0.10 Orphan 116 0 0.0086090 0.7695189 0.7147838
FALSE string skcm.data.2018.09.11 metastatic 0 TRUE 0.10 Elastic Net 41 0 0.0008160 0.6812654 0.6917713
FALSE string skcm.data.2018.09.11 metastatic 0 TRUE 0.10 Hub 43 0 0.0013825 0.6873017 0.7196653
FALSE string skcm.data.2018.09.11 metastatic 0 TRUE 0.10 Orphan 42 0 0.0039169 0.6884032 0.6757322
FALSE string skcm.data.2018.09.11 metastatic 0 TRUE 0.10 Elastic Net 116 0 0.0220258 0.7563888 0.7043236
FALSE string skcm.data.2018.09.11 metastatic 0 TRUE 0.10 Hub 113 0 0.0298483 0.7697832 0.6827057
FALSE string skcm.data.2018.09.11 metastatic 0 TRUE 0.10 Orphan 116 0 0.0086090 0.7695189 0.7147838

4.4 Non-zero genes

4.4.1 Venn Diagram of selected genes

4.4.1.1 Overlap between models (with same target number of variables)

Base model: Elastic Net with Target Vars: 116 and Alpha: 0.10

Base model: Hub with Target Vars: 41 and Alpha: 0.10

Base model: Orphan with Target Vars: 111 and Alpha: 0.10

Table of genes in models

(not running at the moment)

5 5000 Runs

5.1 C-Index distribution

Test set

Summary of C-Index and Log-rank

metric model base.model target.vars alpha mean std median min
C-Index (Test set) Hub Elastic Net 116 0.10 0.624 0.042 0.625 0.473
C-Index (Test set) Hub Hub 41 0.10 0.631 0.042 0.632 0.476
C-Index (Test set) Hub Orphan 111 0.10 0.624 0.042 0.626 0.474
C-Index (Test set) Elastic Net Elastic Net 116 0.10 0.640 0.040 0.641 0.486
C-Index (Test set) Elastic Net Hub 41 0.10 0.648 0.041 0.649 0.474
C-Index (Test set) Elastic Net Orphan 111 0.10 0.641 0.040 0.641 0.487
C-Index (Test set) Orphan Elastic Net 116 0.10 0.645 0.041 0.646 0.48
C-Index (Test set) Orphan Hub 41 0.10 0.645 0.042 0.646 0.468
C-Index (Test set) Orphan Orphan 111 0.10 0.645 0.041 0.646 0.48
Log-rank (Test set) Hub Elastic Net 116 0.10 0.127 0.195 0.043 7.3e-07
Log-rank (Test set) Hub Hub 41 0.10 0.105 0.172 0.030 3.22e-07
Log-rank (Test set) Hub Orphan 111 0.10 0.125 0.193 0.042 7.3e-07
Log-rank (Test set) Elastic Net Elastic Net 116 0.10 0.100 0.171 0.028 1.41e-08
Log-rank (Test set) Elastic Net Hub 41 0.10 0.098 0.169 0.027 5.46e-08
Log-rank (Test set) Elastic Net Orphan 111 0.10 0.099 0.168 0.028 3.01e-08
Log-rank (Test set) Orphan Elastic Net 116 0.10 0.087 0.157 0.020 1.08e-08
Log-rank (Test set) Orphan Hub 41 0.10 0.091 0.161 0.023 4.92e-09
Log-rank (Test set) Orphan Orphan 111 0.10 0.086 0.157 0.021 8.75e-09

C-Index Distribution

Rank

Elastic Net vs Hub
base.model r.squared
Elastic Net with target nvars: 116 alpha: 0.10 0.4719617
Hub with target nvars: 41 alpha: 0.10 0.4067332
Orphan with target nvars: 111 alpha: 0.10 0.4730481

Elastic Net vs. Orphan
base.model r.squared
Elastic Net with target nvars: 116 alpha: 0.10 0.9117127
Hub with target nvars: 41 alpha: 0.10 0.9219959
Orphan with target nvars: 111 alpha: 0.10 0.9130622

Hub vs. Orphan
base.model r.squared
Elastic Net with target nvars: 116 alpha: 0.10 0.4395095
Hub with target nvars: 41 alpha: 0.10 0.4054032
Orphan with target nvars: 111 alpha: 0.10 0.4401935

Train set

Summary of C-Index and Log-rank

metric model base.model target.vars alpha mean std median min
C-Index (Train set) Hub Elastic Net 116 0.10 0.791 0.010 0.791 0.76
C-Index (Train set) Hub Hub 41 0.10 0.707 0.010 0.707 0.673
C-Index (Train set) Hub Orphan 111 0.10 0.786 0.010 0.786 0.754
C-Index (Train set) Elastic Net Elastic Net 116 0.10 0.778 0.010 0.778 0.745
C-Index (Train set) Elastic Net Hub 41 0.10 0.702 0.010 0.702 0.66
C-Index (Train set) Elastic Net Orphan 111 0.10 0.774 0.010 0.774 0.745
C-Index (Train set) Orphan Elastic Net 116 0.10 0.790 0.010 0.790 0.754
C-Index (Train set) Orphan Hub 41 0.10 0.707 0.011 0.707 0.673
C-Index (Train set) Orphan Orphan 111 0.10 0.786 0.010 0.786 0.748
Log-rank (Train set) Hub Elastic Net 116 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Hub Hub 41 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Hub Orphan 111 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Elastic Net 116 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Hub 41 0.10 0.000 0.000 0.000 1.22e-15
Log-rank (Train set) Elastic Net Orphan 111 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Elastic Net 116 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Hub 41 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Orphan 111 0.10 0.000 0.000 0.000 0

C-Index Distribution

C-Index Rank

5.2 Log-rank test on Kaplan-Meier models

5.2.1 Log-Rank distribution

Cumulative

Distribution of Log-rank test with groups separated by high and low risk groups

Distribution

Distribution of Log-rank test with groups separated by high and low risk groups

5.2.2 Log-Rank Rank

5.2.2.1 Elastic Net vs Hub

base.model r.squared
Elastic Net with target nvars: 116 alpha: 0.10 0.1828148
Hub with target nvars: 41 alpha: 0.10 0.1989902
Orphan with target nvars: 111 alpha: 0.10 0.1832092

5.2.2.2 Elastic Net vs. Orphan

base.model r.squared
Elastic Net with target nvars: 116 alpha: 0.10 0.6372866
Hub with target nvars: 41 alpha: 0.10 0.6644938
Orphan with target nvars: 111 alpha: 0.10 0.6347008

5.2.2.3 Hub vs. Orphan

base.model r.squared
Elastic Net with target nvars: 116 alpha: 0.10 0.1585745
Hub with target nvars: 41 alpha: 0.10 0.2080129
Orphan with target nvars: 111 alpha: 0.10 0.1613894

5.3 Consesus genes

5.3.1 Selected genes over all runs

Bar plots of frequencies

Overlap between variables selected

Base model: Elastic Net with Target Vars: 116 and Alpha: 0.10

Base model: Hub with Target Vars: 41 and Alpha: 0.10

Base model: Orphan with Target Vars: 111 and Alpha: 0.10

5.3.2 Selected genes in significant runs

i.e. with pvalue < 0.05 in Log-rank test using the test set.

Bar plots of frequencies

Overlap between variables selected

5.3.2.0.1 Base model Elastic Net with target nvars: 0.10 alpha: 116

5.3.2.0.2 Base model Hub with target nvars: 0.10 alpha: 41

5.3.2.0.3 Base model Orphan with target nvars: 0.10 alpha: 111

5.3.3 Genes in Significant runs

i.e. with pvalue < 0.05 in Log-rank test using the test set.

Top consensus 20 genes

Gene Overlap total
ENSG00000140511 2 18861
ENSG00000189013 2 18829
ENSG00000108700 2 18743
ENSG00000185885 2 17282
ENSG00000174885 2 15713
ENSG00000159618 2 15272
ENSG00000156265 2 14971
ENSG00000204642 2 14514
ENSG00000100918 2 13128
ENSG00000231389 2 12455
ENSG00000178977 2 12346
ENSG00000089486 2 12301
ENSG00000213145 2 12165
ENSG00000085831 3 11826
ENSG00000206053 2 11819
ENSG00000135114 2 11815
ENSG00000120910 2 11675
ENSG00000183850 2 11635
ENSG00000162645 2 11614
ENSG00000168734 2 11380

All Genes

ENSG00000140511(18861), ENSG00000189013(18829), ENSG00000108700(18743), ENSG00000185885(17282), ENSG00000174885(15713), ENSG00000159618(15272), ENSG00000156265(14971), ENSG00000204642(14514), ENSG00000100918(13128), ENSG00000231389(12455), ENSG00000178977(12346), ENSG00000089486(12301), ENSG00000213145(12165), ENSG00000085831(11826), ENSG00000206053(11819), ENSG00000135114(11815), ENSG00000120910(11675), ENSG00000183850(11635), ENSG00000162645(11614), ENSG00000168734(11380), ENSG00000271503(11180), ENSG00000146618(11102), ENSG00000185880(10727), ENSG00000185933(10696), ENSG00000112039(10504), ENSG00000157404(10311), ENSG00000016082(10211), ENSG00000196735(10201), ENSG00000188282(10104), ENSG00000099399(10060), ENSG00000197251(10058), ENSG00000132744(9858), ENSG00000206337(9826), ENSG00000165182(9485), ENSG00000141437(9298), ENSG00000278540(9235), ENSG00000126458(9177), ENSG00000275763(8830), ENSG00000169507(8795), ENSG00000140853(8783), ENSG00000150991(8775), ENSG00000117148(8746), ENSG00000162063(8746), ENSG00000258653(8734), ENSG00000275302(8673), ENSG00000198502(8640), ENSG00000100911(8608), ENSG00000186891(8584), ENSG00000059378(8472), ENSG00000213578(8458), ENSG00000215012(8449), ENSG00000089127(8443), ENSG00000146858(8434), ENSG00000144460(8426), ENSG00000169249(8426), ENSG00000226025(8369), ENSG00000112062(8301), ENSG00000163631(8287), ENSG00000090339(8274), ENSG00000179344(8274), ENSG00000089692(8262), ENSG00000204287(8252), ENSG00000146648(8239), ENSG00000273136(8183), ENSG00000148386(8151), ENSG00000171180(8097), ENSG00000135355(8078), ENSG00000196126(8040), ENSG00000137267(7967), ENSG00000111801(7718), ENSG00000248385(7678), ENSG00000188906(7605), ENSG00000223865(7592), ENSG00000129472(7530), ENSG00000153563(7508), ENSG00000074181(7382), ENSG00000122304(7262), ENSG00000143469(7246), ENSG00000149781(7010), ENSG00000249948(6872), ENSG00000176083(6790), ENSG00000179583(6786), ENSG00000140534(6648), ENSG00000182986(6631), ENSG00000169953(6563), ENSG00000097096(6541), ENSG00000127616(6358), ENSG00000186150(6223), ENSG00000197536(6190), ENSG00000178927(6117), ENSG00000183559(6032), ENSG00000134321(5975), ENSG00000111640(5967), ENSG00000196081(5948), ENSG00000166710(5924), ENSG00000154438(5883), ENSG00000183155(5847), ENSG00000172671(5836), ENSG00000204257(5819), ENSG00000180616(5797), ENSG00000135446(5761), ENSG00000183795(5721), ENSG00000253276(5719), ENSG00000197122(5653), ENSG00000091831(5648), ENSG00000187608(5586), ENSG00000102743(5522), ENSG00000164270(5520), ENSG00000205978(5511), ENSG00000100300(5497), ENSG00000171105(5433), ENSG00000105617(5422), ENSG00000184471(5397), ENSG00000258818(5385), ENSG00000169248(5353), ENSG00000213886(5348), ENSG00000160803(5328), ENSG00000125363(5322), ENSG00000134153(5309), ENSG00000080824(5304), ENSG00000005249(5281), ENSG00000102178(5276), ENSG00000126785(5240), ENSG00000105357(5231), ENSG00000183795(5230), ENSG00000253831(5208), ENSG00000072062(5200), ENSG00000126803(5184), ENSG00000074800(5156), ENSG00000129682(5140), ENSG00000019582(5079), ENSG00000122728(5076), ENSG00000204252(5068), ENSG00000010295(5065), ENSG00000182866(5022), ENSG00000127418(4992), ENSG00000127472(4979), ENSG00000132698(4942), ENSG00000113721(4940), ENSG00000084774(4927), ENSG00000171345(4857), ENSG00000131203(4846), ENSG00000229474(4835), ENSG00000105374(4828), ENSG00000149806(4818), ENSG00000126583(4790), ENSG00000241106(4731), ENSG00000141510(4729), ENSG00000177989(4699), ENSG00000182749(4694), ENSG00000132170(4685), ENSG00000103356(4630), ENSG00000136003(4607), ENSG00000109193(4594), ENSG00000165782(4587), ENSG00000112139(4586), ENSG00000134253(4576), ENSG00000268107(4565), ENSG00000189377(4563), ENSG00000104140(4511), ENSG00000157884(4500), ENSG00000114491(4483), ENSG00000077080(4466), ENSG00000170325(4461), ENSG00000176894(4458), ENSG00000205835(4427), ENSG00000067560(4399), ENSG00000157600(4392), ENSG00000179796(4364), ENSG00000110975(4363), ENSG00000196684(4333), ENSG00000138413(4326), ENSG00000124256(4281), ENSG00000153790(4274), ENSG00000255432(4257), ENSG00000198515(4237), ENSG00000177606(4229), ENSG00000118473(4187), ENSG00000203499(4186), ENSG00000177143(4180), ENSG00000168036(4177), ENSG00000170312(4152), ENSG00000196335(4142), ENSG00000125347(4080), ENSG00000128342(4074), ENSG00000100030(4019), ENSG00000159899(3993), ENSG00000229205(3973), ENSG00000213215(3971), ENSG00000138613(3962), ENSG00000010810(3889), ENSG00000229676(3867), ENSG00000116455(3840), ENSG00000162595(3837), ENSG00000170476(3820), ENSG00000138613(3812), ENSG00000142089(3795), ENSG00000145936(3754), ENSG00000111335(3750), ENSG00000196358(3750), ENSG00000185379(3728), ENSG00000174446(3716), ENSG00000169515(3701), ENSG00000163632(3699), ENSG00000100302(3692), ENSG00000162654(3682), ENSG00000148156(3681), ENSG00000178035(3675), ENSG00000027644(3607), ENSG00000214087(3606), ENSG00000166415(3591), ENSG00000142208(3565), ENSG00000141736(3551), ENSG00000101457(3539), ENSG00000217442(3537), ENSG00000134684(3525), ENSG00000182050(3521), ENSG00000185933(3475), ENSG00000169906(3458), ENSG00000221963(3454), ENSG00000170315(3436), ENSG00000165584(3412), ENSG00000174775(3389), ENSG00000183421(3382), ENSG00000204371(3348), ENSG00000102882(3301), ENSG00000123201(3275), ENSG00000174899(3250), ENSG00000141668(3240), ENSG00000124226(3239), ENSG00000185585(3237), ENSG00000128891(3220), ENSG00000080503(3193), ENSG00000142621(3190), ENSG00000250317(3124), ENSG00000168925(3098), ENSG00000186458(3097), ENSG00000156575(3094), ENSG00000085831(3073), ENSG00000126752(3036), ENSG00000166710(3025), ENSG00000025423(3019), ENSG00000222038(3014), ENSG00000167244(3003), ENSG00000123374(2992), ENSG00000049247(2985), ENSG00000104325(2962), ENSG00000213886(2962), ENSG00000047578(2960), ENSG00000168925(2934), ENSG00000124721(2923), ENSG00000166523(2920), ENSG00000167077(2893), ENSG00000145936(2876), ENSG00000126790(2876), ENSG00000154928(2876), ENSG00000107758(2839), ENSG00000115085(2837), ENSG00000115073(2824), ENSG00000063180(2762), ENSG00000197587(2759), ENSG00000102178(2755), ENSG00000169245(2752), ENSG00000151883(2749), ENSG00000167011(2749), ENSG00000104833(2743), ENSG00000169750(2743), ENSG00000253313(2741), ENSG00000006451(2741), ENSG00000132915(2739), ENSG00000008853(2718), ENSG00000119917(2710), ENSG00000215386(2701), ENSG00000124782(2645), ENSG00000106436(2623), ENSG00000137842(2615), ENSG00000186603(2600), ENSG00000214274(2597), ENSG00000174697(2594), ENSG00000196834(2583), ENSG00000169248(2567), ENSG00000117266(2564), ENSG00000124227(2554), ENSG00000052795(2545), ENSG00000163121(2538), ENSG00000169507(2536), ENSG00000143632(2534), ENSG00000198668(2532), ENSG00000197891(2530), ENSG00000197272(2520), ENSG00000181847(2515), ENSG00000204116(2515), ENSG00000168268(2492), ENSG00000080824(2484), ENSG00000228741(2472), ENSG00000140368(2448), ENSG00000206072(2446), ENSG00000169717(2441), ENSG00000232629(2389), ENSG00000165949(2354), ENSG00000167476(2352), ENSG00000155366(2352), ENSG00000198793(2350), ENSG00000105976(2349), ENSG00000111206(2325), ENSG00000167183(2310), ENSG00000126785(2283), ENSG00000105357(2272), ENSG00000183785(2268), ENSG00000164885(2267), ENSG00000140463(2261), ENSG00000204928(2249), ENSG00000258989(2244), ENSG00000141510(2241), ENSG00000159251(2240), ENSG00000119922(2228), ENSG00000254505(2207), ENSG00000138755(2204), ENSG00000254647(2204), ENSG00000072133(2203), ENSG00000182583(2200), ENSG00000213967(2184), ENSG00000141437(2178), ENSG00000116663(2174), ENSG00000143185(2171), ENSG00000078487(2164), ENSG00000128383(2155), ENSG00000237787(2152), ENSG00000150676(2124), ENSG00000173626(2107), ENSG00000188130(2107), ENSG00000276644(2106), ENSG00000007264(2098), ENSG00000171105(2095), ENSG00000111335(2081), ENSG00000166833(2065), ENSG00000142102(2061), ENSG00000095794(2045), ENSG00000274180(2042), ENSG00000137496(2039), ENSG00000255330(2030), ENSG00000204006(2005), ENSG00000176490(2002), ENSG00000177504(1997), ENSG00000074966(1995), ENSG00000137959(1973), ENSG00000180745(1960), ENSG00000173401(1955), ENSG00000188389(1953), ENSG00000250550(1934), ENSG00000126583(1926), ENSG00000078142(1925), ENSG00000229674(1923), ENSG00000007171(1919), ENSG00000106571(1917), ENSG00000225526(1913), ENSG00000232810(1911), ENSG00000204290(1900), ENSG00000136048(1899), ENSG00000100342(1896), ENSG00000176040(1894), ENSG00000170345(1881), ENSG00000100422(1877), ENSG00000092096(1874), ENSG00000068400(1873), ENSG00000105370(1851), ENSG00000221953(1846), ENSG00000177508(1838), ENSG00000234745(1815), ENSG00000198520(1803), ENSG00000188612(1783), ENSG00000077080(1781), ENSG00000163293(1769), ENSG00000198678(1769), ENSG00000105329(1758), ENSG00000068985(1757), ENSG00000185262(1750), ENSG00000176635(1745), ENSG00000129559(1745), ENSG00000156284(1734), ENSG00000108551(1726), ENSG00000275778(1724), ENSG00000205916(1720), ENSG00000171729(1717), ENSG00000164867(1710), ENSG00000115523(1698), ENSG00000187553(1696), ENSG00000214050(1690), ENSG00000166828(1687), ENSG00000155875(1686), ENSG00000254692(1684), ENSG00000154451(1682), ENSG00000127472(1669), ENSG00000139572(1668), ENSG00000148602(1666), ENSG00000136238(1665), ENSG00000134398(1664), ENSG00000104129(1655), ENSG00000187483(1651), ENSG00000214140(1651), ENSG00000092820(1624), ENSG00000112592(1620), ENSG00000227868(1619), ENSG00000101421(1617), ENSG00000149809(1615), ENSG00000186470(1611), ENSG00000133256(1610), ENSG00000177673(1609), ENSG00000120217(1604), ENSG00000140564(1592), ENSG00000175505(1590), ENSG00000260092(1586), ENSG00000179219(1584), ENSG00000131966(1583), ENSG00000196712(1580), ENSG00000215343(1575), ENSG00000151327(1558), ENSG00000258311(1557), ENSG00000107249(1553), ENSG00000100139(1548), ENSG00000204779(1548), ENSG00000138685(1535), ENSG00000150456(1533), ENSG00000101082(1532), ENSG00000163909(1530), ENSG00000112186(1528), ENSG00000218336(1518), ENSG00000101266(1515), ENSG00000129514(1510), ENSG00000102096(1509), ENSG00000110711(1501), ENSG00000125826(1496), ENSG00000196182(1477), ENSG00000157613(1475), ENSG00000134250(1469), ENSG00000141194(1465), ENSG00000111537(1459), ENSG00000243749(1455), ENSG00000171219(1443), ENSG00000274020(1419), ENSG00000184351(1417), ENSG00000167123(1412), ENSG00000139083(1405), ENSG00000165731(1400), ENSG00000249581(1398), ENSG00000180616(1391), ENSG00000147647(1383), ENSG00000118513(1377), ENSG00000179930(1371), ENSG00000259399(1365), ENSG00000128335(1363), ENSG00000147262(1360), ENSG00000232859(1353), ENSG00000182795(1352), ENSG00000064270(1347), ENSG00000164742(1346), ENSG00000137824(1344), ENSG00000134539(1343), ENSG00000066468(1340), ENSG00000213714(1335), ENSG00000243130(1335), ENSG00000116981(1325), ENSG00000101017(1323), ENSG00000187003(1318), ENSG00000171552(1310), ENSG00000130477(1308), ENSG00000175520(1308), ENSG00000102385(1301), ENSG00000181355(1298), ENSG00000162039(1297), ENSG00000150457(1292), ENSG00000159131(1292), ENSG00000185386(1292), ENSG00000173421(1289), ENSG00000253831(1287), ENSG00000136997(1287), ENSG00000188191(1287), ENSG00000010219(1285), ENSG00000048052(1285), ENSG00000100453(1278), ENSG00000127951(1277), ENSG00000171180(1276), ENSG00000175550(1276), ENSG00000132141(1273), ENSG00000186765(1269), ENSG00000110987(1265), ENSG00000185028(1263), ENSG00000180999(1262), ENSG00000267041(1260), ENSG00000141736(1260), ENSG00000178021(1260), ENSG00000124587(1250), ENSG00000174938(1248), ENSG00000130675(1247), ENSG00000257127(1246), ENSG00000077782(1246), ENSG00000167553(1239), ENSG00000113721(1227), ENSG00000253958(1226), ENSG00000111331(1221), ENSG00000139656(1220), ENSG00000104783(1216), ENSG00000128408(1213), ENSG00000204592(1212), ENSG00000186827(1210), ENSG00000250506(1209), ENSG00000262576(1206), ENSG00000110195(1199), ENSG00000183258(1196), ENSG00000178950(1191), ENSG00000128203(1176), ENSG00000206069(1176), ENSG00000049769(1167), ENSG00000170315(1145), ENSG00000198947(1144), ENSG00000117228(1141), ENSG00000068305(1141), ENSG00000130635(1134), ENSG00000106976(1129), ENSG00000100031(1126), ENSG00000267710(1124), ENSG00000121690(1123), ENSG00000179388(1117), ENSG00000128789(1095), ENSG00000179958(1095), ENSG00000197915(1093), ENSG00000147481(1089), ENSG00000203784(1080), ENSG00000238269(1079), ENSG00000069431(1077), ENSG00000144354(1071), ENSG00000102755(1071), ENSG00000140612(1067), ENSG00000128394(1066), ENSG00000234409(1064), ENSG00000183054(1060), ENSG00000138669(1059), ENSG00000138669(1059), ENSG00000026950(1058), ENSG00000177084(1056), ENSG00000179348(1055), ENSG00000064201(1047), ENSG00000198794(1039), ENSG00000162976(1035), ENSG00000277481(1034), ENSG00000230510(1033), ENSG00000104518(1031), ENSG00000186496(1030), ENSG00000092010(1029), ENSG00000136869(1028), ENSG00000172543(1027), ENSG00000189143(1026), ENSG00000138496(1025), ENSG00000125975(1024), ENSG00000213928(1010), ENSG00000164270(1007), ENSG00000128045(1005), ENSG00000099999(1003), ENSG00000105221(1003), ENSG00000180090(1000), ENSG00000130528(995), ENSG00000104714(993), ENSG00000127249(990), ENSG00000234745(990), ENSG00000130723(987), ENSG00000178950(975), ENSG00000165182(973), ENSG00000154451(973), ENSG00000119403(969), ENSG00000126561(969), ENSG00000141448(969), ENSG00000196408(965), ENSG00000168404(960), ENSG00000232973(959), ENSG00000154358(956), ENSG00000167491(949), ENSG00000139899(948), ENSG00000099399(944), ENSG00000134853(939), ENSG00000104325(937), ENSG00000096968(937), ENSG00000174226(936), ENSG00000205352(935), ENSG00000118515(933), ENSG00000183248(931), ENSG00000280433(925), ENSG00000107175(922), ENSG00000176209(922), ENSG00000181873(914), ENSG00000118894(912), ENSG00000181409(904), ENSG00000176563(902), ENSG00000081760(901), ENSG00000175946(899), ENSG00000143891(895), ENSG00000165175(895), ENSG00000239920(891), ENSG00000198832(886), ENSG00000280670(885), ENSG00000136244(885), ENSG00000176095(884), ENSG00000185038(882), ENSG00000062485(867), ENSG00000180440(865), ENSG00000226023(863), ENSG00000010030(860), ENSG00000213793(860), ENSG00000146618(859), ENSG00000110042(854), ENSG00000133943(853), ENSG00000128191(850), ENSG00000102539(840), ENSG00000005339(836), ENSG00000161944(836), ENSG00000152214(836), ENSG00000267477(835), ENSG00000183629(829), ENSG00000148444(828), ENSG00000075673(826), ENSG00000150556(823), ENSG00000196422(823), ENSG00000215187(820), ENSG00000005022(816), ENSG00000213281(816), ENSG00000197233(813), ENSG00000132535(810), ENSG00000187653(808), ENSG00000186908(807), ENSG00000106541(805), ENSG00000168610(805), ENSG00000075624(800), ENSG00000196388(794), ENSG00000163958(791), ENSG00000171428(791), ENSG00000174939(790), ENSG00000139364(789), ENSG00000204525(788), ENSG00000163346(786), ENSG00000178568(784), ENSG00000226792(784), ENSG00000151577(781), ENSG00000128463(781), ENSG00000126456(775), ENSG00000181222(772), ENSG00000275896(772), ENSG00000184378(772), ENSG00000188219(771), ENSG00000185630(770), ENSG00000115073(770), ENSG00000181617(764), ENSG00000176387(763), ENSG00000181264(760), ENSG00000184560(755), ENSG00000196230(751), ENSG00000236334(750), ENSG00000157782(750), ENSG00000023839(747), ENSG00000196421(745), ENSG00000162595(745), ENSG00000156234(742), ENSG00000105220(741), ENSG00000130487(741), ENSG00000014914(740), ENSG00000168582(735), ENSG00000143199(734), ENSG00000120217(727), ENSG00000085840(726), ENSG00000196411(724), ENSG00000166851(720), ENSG00000128284(718), ENSG00000138031(717), ENSG00000197265(715), ENSG00000119401(712), ENSG00000156711(712), ENSG00000165233(710), ENSG00000178287(710), ENSG00000115112(706), ENSG00000198633(706), ENSG00000204700(705), ENSG00000001626(702), ENSG00000180644(702), ENSG00000121691(698), ENSG00000142748(697), ENSG00000243649(696), ENSG00000105519(694), ENSG00000152822(691), ENSG00000181798(687), ENSG00000103496(687), ENSG00000160908(686), ENSG00000186153(681), ENSG00000247626(677), ENSG00000173762(675), ENSG00000169067(671), ENSG00000126456(668), ENSG00000157765(666), ENSG00000163812(665), ENSG00000147457(663), ENSG00000196748(662), ENSG00000108511(661), ENSG00000164188(661), ENSG00000159723(659), ENSG00000172139(659), ENSG00000171217(658), ENSG00000257446(658), ENSG00000139160(657), ENSG00000204070(656), ENSG00000171116(653), ENSG00000251184(653), ENSG00000131097(651), ENSG00000137486(644), ENSG00000137501(641), ENSG00000279782(641), ENSG00000255302(640), ENSG00000157551(639), ENSG00000133687(638), ENSG00000176871(638), ENSG00000185888(636), ENSG00000134046(633), ENSG00000196240(630), ENSG00000008197(630), ENSG00000185532(629), ENSG00000239713(628), ENSG00000115274(626), ENSG00000134539(626), ENSG00000003989(625), ENSG00000071575(622), ENSG00000158480(620), ENSG00000204632(617), ENSG00000112877(616), ENSG00000243501(616), ENSG00000059758(615), ENSG00000198478(612), ENSG00000182168(610), ENSG00000101470(609), ENSG00000129460(608), ENSG00000140519(608), ENSG00000099139(608), ENSG00000133703(607), ENSG00000100206(603), ENSG00000102221(602), ENSG00000278463(602), ENSG00000272162(601), ENSG00000204315(601), ENSG00000145113(598), ENSG00000116478(598), ENSG00000196843(594), ENSG00000255524(592), ENSG00000118292(589), ENSG00000122643(589), ENSG00000198643(589), ENSG00000115592(589), ENSG00000005471(584), ENSG00000179058(584), ENSG00000167306(582), ENSG00000104388(581), ENSG00000148156(568), ENSG00000215883(564), ENSG00000055813(559), ENSG00000016402(558), ENSG00000168234(557), ENSG00000171793(556), ENSG00000196440(556), ENSG00000107731(555), ENSG00000157833(555), ENSG00000183185(555), ENSG00000164123(554), ENSG00000066230(553), ENSG00000177885(552), ENSG00000101470(551), ENSG00000135447(550), ENSG00000160752(550), ENSG00000167985(550), ENSG00000076248(549), ENSG00000181036(549), ENSG00000088320(546), ENSG00000181085(542), ENSG00000154319(539), ENSG00000103496(538), ENSG00000214866(536), ENSG00000100450(535), ENSG00000132471(535), ENSG00000112715(535), ENSG00000229571(535), ENSG00000115325(533), ENSG00000184611(533), ENSG00000196431(533), ENSG00000120322(532), ENSG00000162639(528), ENSG00000167588(527), ENSG00000198033(526), ENSG00000105963(524), ENSG00000165868(521), ENSG00000213999(518), ENSG00000196683(513), ENSG00000127585(512), ENSG00000019991(510), ENSG00000197016(510), ENSG00000150054(509), ENSG00000205089(508), ENSG00000183878(506), ENSG00000033327(505), ENSG00000129055(498), ENSG00000171722(498), ENSG00000100302(498), ENSG00000183166(498), ENSG00000135480(494), ENSG00000169436(493), ENSG00000213889(493), ENSG00000056487(492), ENSG00000196511(492), ENSG00000092853(491), ENSG00000184675(489), ENSG00000219435(484), ENSG00000185252(481), ENSG00000161544(480), ENSG00000043591(480), ENSG00000165643(478), ENSG00000134057(478), ENSG00000130813(476), ENSG00000173757(476), ENSG00000138823(473), ENSG00000154269(470), ENSG00000103522(470), ENSG00000164543(468), ENSG00000151150(467), ENSG00000167004(465), ENSG00000181786(465), ENSG00000181467(462), ENSG00000183864(461), ENSG00000157884(460), ENSG00000142279(459), ENSG00000168062(457), ENSG00000171862(456), ENSG00000271079(452), ENSG00000178445(452), ENSG00000177054(452), ENSG00000167531(449), ENSG00000134326(449), ENSG00000243772(448), ENSG00000177508(448), ENSG00000091513(448), ENSG00000054793(447), ENSG00000131153(447), ENSG00000185219(444), ENSG00000261678(444), ENSG00000100029(442), ENSG00000236279(441), ENSG00000085563(435), ENSG00000235750(434), ENSG00000011451(433), ENSG00000168928(433), ENSG00000236446(432), ENSG00000128340(431), ENSG00000021645(430), ENSG00000146910(430), ENSG00000184735(430), ENSG00000198157(430), ENSG00000256100(430), ENSG00000189431(429), ENSG00000164045(424), ENSG00000008083(423), ENSG00000188580(423), ENSG00000148400(421), ENSG00000176269(420), ENSG00000198700(418), ENSG00000104447(415), ENSG00000127663(415), ENSG00000185122(414), ENSG00000033170(413), ENSG00000092010(413), ENSG00000137513(412), ENSG00000225973(412), ENSG00000254706(410), ENSG00000259330(410), ENSG00000178965(409), ENSG00000114854(408), ENSG00000143569(407), ENSG00000253910(407), ENSG00000101109(406), ENSG00000240230(405), ENSG00000214872(403), ENSG00000114529(402), ENSG00000255561(401), ENSG00000141867(400), ENSG00000063438(399), ENSG00000132792(399), ENSG00000089012(398), ENSG00000110799(396), ENSG00000166527(396), ENSG00000101213(394), ENSG00000072274(393), ENSG00000175395(393), ENSG00000100985(393), ENSG00000108830(392), ENSG00000279956(388), ENSG00000081189(387), ENSG00000083814(386), ENSG00000212916(386), ENSG00000183844(385), ENSG00000189037(385), ENSG00000187821(383), ENSG00000159884(382), ENSG00000126709(381), ENSG00000172183(381), ENSG00000173821(380), ENSG00000281613(379), ENSG00000244020(378), ENSG00000006530(377), ENSG00000185475(377), ENSG00000101438(377), ENSG00000160193(377), ENSG00000126803(376), ENSG00000156381(375), ENSG00000130433(374), ENSG00000141946(374), ENSG00000139292(373), ENSG00000166913(372), ENSG00000186810(370), ENSG00000261210(369), ENSG00000184009(369), ENSG00000173077(368), ENSG00000081853(367), ENSG00000221957(366), ENSG00000103355(365), ENSG00000253649(365), ENSG00000183117(362), ENSG00000176165(362), ENSG00000167550(362), ENSG00000085999(361), ENSG00000163564(361), ENSG00000205057(361), ENSG00000087303(360), ENSG00000122035(355), ENSG00000138107(355), ENSG00000166484(355), ENSG00000137101(353), ENSG00000143674(352), ENSG00000117228(351), ENSG00000120332(350), ENSG00000196542(349), ENSG00000197046(349), ENSG00000124641(346), ENSG00000128655(346), ENSG00000091490(345), ENSG00000129250(345), ENSG00000166548(343), ENSG00000135052(342), ENSG00000158195(342), ENSG00000125166(342), ENSG00000013364(341), ENSG00000039068(341), ENSG00000012171(340), ENSG00000196981(340), ENSG00000109084(339), ENSG00000105499(337), ENSG00000147144(337), ENSG00000278705(337), ENSG00000186881(336), ENSG00000137571(335), ENSG00000104695(334), ENSG00000065320(333), ENSG00000153898(333), ENSG00000140464(333), ENSG00000113448(333), ENSG00000124762(332), ENSG00000137672(331), ENSG00000164171(331), ENSG00000005981(329), ENSG00000249860(329), ENSG00000138162(328), ENSG00000008853(328), ENSG00000168899(326), ENSG00000092377(325), ENSG00000117215(325), ENSG00000133398(325), ENSG00000171864(325), ENSG00000102225(324), ENSG00000095066(323), ENSG00000104365(323), ENSG00000168243(323), ENSG00000127955(322), ENSG00000132170(321), ENSG00000131747(321), ENSG00000185963(320), ENSG00000215910(320), ENSG00000243649(319), ENSG00000239306(319), ENSG00000214274(319), ENSG00000132821(316), ENSG00000153721(316), ENSG00000155287(315), ENSG00000237988(315), ENSG00000179142(315), ENSG00000258653(314), ENSG00000154153(313), ENSG00000094631(313), ENSG00000196081(312), ENSG00000076826(311), ENSG00000102387(311), ENSG00000164142(309), ENSG00000205220(309), ENSG00000122644(309), ENSG00000183117(307), ENSG00000172322(307), ENSG00000025423(307), ENSG00000100154(307), ENSG00000122145(306), ENSG00000144481(305), 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ENSG00000124701(2), ENSG00000125650(2), ENSG00000127252(2), ENSG00000127743(2), ENSG00000127995(2), ENSG00000129646(2), ENSG00000130695(2), ENSG00000131037(2), ENSG00000131068(2), ENSG00000131233(2), ENSG00000131669(2), ENSG00000132429(2), ENSG00000133107(2), ENSG00000133134(2), ENSG00000133328(2), ENSG00000134297(2), ENSG00000134612(2), ENSG00000136542(2), ENSG00000137098(2), ENSG00000139767(2), ENSG00000143641(2), ENSG00000144410(2), ENSG00000144815(2), ENSG00000145194(2), ENSG00000145708(2), ENSG00000147027(2), ENSG00000148481(2), ENSG00000151388(2), ENSG00000151445(2), ENSG00000154760(2), ENSG00000155034(2), ENSG00000155622(2), ENSG00000157653(2), ENSG00000160325(2), ENSG00000160392(2), ENSG00000163013(2), ENSG00000163328(2), ENSG00000163444(2), ENSG00000163898(2), ENSG00000164054(2), ENSG00000165685(2), ENSG00000166145(2), ENSG00000166750(2), ENSG00000167646(2), ENSG00000168778(2), ENSG00000169085(2), ENSG00000169181(2), ENSG00000170265(2), ENSG00000170417(2), ENSG00000170777(2), ENSG00000171243(2), ENSG00000171357(2), ENSG00000172775(2), ENSG00000173715(2), ENSG00000174403(2), ENSG00000174448(2), ENSG00000175984(2), ENSG00000176435(2), ENSG00000176595(2), ENSG00000176641(2), ENSG00000176971(2), ENSG00000177576(2), ENSG00000177679(2), ENSG00000177946(2), ENSG00000179057(2), ENSG00000179304(2), ENSG00000179526(2), ENSG00000181240(2), ENSG00000181378(2), ENSG00000182327(2), ENSG00000183396(2), ENSG00000183666(2), ENSG00000183853(2), ENSG00000184208(2), ENSG00000184716(2), ENSG00000185156(2), ENSG00000186281(2), ENSG00000186297(2), ENSG00000186648(2), ENSG00000186792(2), ENSG00000186825(2), ENSG00000187123(2), ENSG00000187288(2), ENSG00000188707(2), ENSG00000188760(2), ENSG00000188959(2), ENSG00000189157(2), ENSG00000189182(2), ENSG00000196312(2), ENSG00000196576(2), ENSG00000196800(2), ENSG00000196990(2), ENSG00000197364(2), ENSG00000197568(2), ENSG00000197617(2), ENSG00000197870(2), ENSG00000198003(2), ENSG00000198824(2), ENSG00000198883(2), ENSG00000204183(2), ENSG00000204347(2), ENSG00000205002(2), ENSG00000205464(2), ENSG00000205869(2), ENSG00000206557(2), ENSG00000213920(2), ENSG00000214413(2), ENSG00000214414(2), ENSG00000214617(2), ENSG00000214652(2), ENSG00000214694(2), ENSG00000215196(2), ENSG00000223658(2), ENSG00000224186(2), ENSG00000224807(2), ENSG00000226763(2), ENSG00000230426(2), ENSG00000232125(2), ENSG00000235453(2), ENSG00000237651(2), ENSG00000238210(2), ENSG00000240225(2), ENSG00000240764(2), ENSG00000241224(2), ENSG00000242221(2), ENSG00000243244(2), ENSG00000243696(2), ENSG00000244234(2), ENSG00000249992(2), ENSG00000250709(2), ENSG00000255819(2), ENSG00000255872(2), ENSG00000256966(2), ENSG00000259571(2), ENSG00000262304(2), ENSG00000267303(2), ENSG00000269713(2), ENSG00000270629(2), ENSG00000271043(2), ENSG00000271723(2), ENSG00000272899(2), ENSG00000274600(2), ENSG00000274808(2), ENSG00000275674(2), ENSG00000275700(2), ENSG00000277150(2), ENSG00000277322(2), ENSG00000278615(2), ENSG00000279073(2), ENSG00000279078(2), ENSG00000279493(2), ENSG00000130755(2), ENSG00000137767(2), ENSG00000152766(2), ENSG00000173193(2), ENSG00000109943(2), ENSG00000138413(1), ENSG00000237787(1), ENSG00000177504(1), ENSG00000204290(1), ENSG00000163293(1), ENSG00000177673(1), ENSG00000173421(1), ENSG00000185028(1), ENSG00000180999(1), ENSG00000262576(1), ENSG00000198947(1), ENSG00000179348(1), ENSG00000180090(1), ENSG00000130528(1), ENSG00000127249(1), ENSG00000126561(1), ENSG00000110042(1), ENSG00000183629(1), ENSG00000196388(1), ENSG00000157765(1), ENSG00000196748(1), ENSG00000159723(1), ENSG00000204070(1), ENSG00000131097(1), ENSG00000157551(1), ENSG00000158480(1), ENSG00000198478(1), ENSG00000182168(1), ENSG00000255524(1), ENSG00000107731(1), ENSG00000164123(1), ENSG00000132471(1), ENSG00000167588(1), ENSG00000127585(1), ENSG00000171722(1), ENSG00000219435(1), ENSG00000198157(1), ENSG00000127663(1), ENSG00000132792(1), ENSG00000212916(1), ENSG00000159884(1), ENSG00000281613(1), ENSG00000244020(1), ENSG00000095066(1), ENSG00000168243(1), ENSG00000102387(1), ENSG00000164142(1), ENSG00000187676(1), ENSG00000242019(1), ENSG00000008394(1), ENSG00000232388(1), ENSG00000102554(1), ENSG00000271793(1), ENSG00000273167(1), ENSG00000163209(1), ENSG00000170390(1), ENSG00000101425(1), ENSG00000159263(1), ENSG00000224940(1), ENSG00000181396(1), ENSG00000205858(1), ENSG00000215193(1), ENSG00000244242(1), ENSG00000167601(1), ENSG00000106012(1), ENSG00000187957(1), ENSG00000118729(1), ENSG00000166987(1), ENSG00000172738(1), ENSG00000261456(1), ENSG00000149090(1), ENSG00000172717(1), ENSG00000215717(1), ENSG00000075702(1), ENSG00000140950(1), ENSG00000168273(1), ENSG00000135324(1), ENSG00000114867(1), ENSG00000149499(1), ENSG00000181007(1), ENSG00000180834(1), ENSG00000135245(1), ENSG00000130119(1), ENSG00000188056(1), ENSG00000272196(1), ENSG00000189320(1), ENSG00000203870(1), ENSG00000204514(1), ENSG00000204713(1), ENSG00000186326(1), ENSG00000198221(1), ENSG00000126602(1), ENSG00000259417(1), ENSG00000176845(1), ENSG00000148803(1), ENSG00000140264(1), ENSG00000147588(1), ENSG00000160932(1), ENSG00000133433(1), ENSG00000183763(1), ENSG00000184368(1), ENSG00000106853(1), ENSG00000176619(1), ENSG00000124508(1), ENSG00000075218(1), ENSG00000167747(1), ENSG00000133872(1), ENSG00000183779(1), ENSG00000112559(1), ENSG00000154102(1), ENSG00000127419(1), ENSG00000172932(1), ENSG00000203778(1), ENSG00000223820(1), ENSG00000104825(1), ENSG00000196460(1), ENSG00000068654(1), ENSG00000157927(1), ENSG00000111424(1), ENSG00000186212(1), ENSG00000239887(1), ENSG00000180357(1), ENSG00000123892(1), ENSG00000165169(1), ENSG00000261857(1), ENSG00000162139(1), ENSG00000197448(1), ENSG00000268182(1), ENSG00000159184(1), ENSG00000008283(1), ENSG00000130147(1), ENSG00000147439(1), ENSG00000117226(1), ENSG00000073331(1), ENSG00000180229(1), ENSG00000160679(1), ENSG00000170627(1), ENSG00000182108(1), ENSG00000213445(1), ENSG00000125148(1), ENSG00000162512(1), ENSG00000183496(1), ENSG00000187122(1), ENSG00000101363(1), ENSG00000115008(1), ENSG00000121314(1), ENSG00000128683(1), ENSG00000213512(1), ENSG00000087157(1), ENSG00000102924(1), ENSG00000130643(1), ENSG00000132010(1), ENSG00000143158(1), ENSG00000164932(1), ENSG00000176919(1), ENSG00000179820(1), ENSG00000183826(1), ENSG00000197430(1), ENSG00000198542(1), ENSG00000243207(1), ENSG00000183833(1), ENSG00000091583(1), ENSG00000092068(1), ENSG00000106066(1), ENSG00000115844(1), ENSG00000116983(1), ENSG00000117601(1), ENSG00000118181(1), ENSG00000118194(1), ENSG00000127774(1), ENSG00000128578(1), ENSG00000129910(1), ENSG00000132382(1), ENSG00000133026(1), ENSG00000136943(1), ENSG00000138207(1), ENSG00000141505(1), ENSG00000141576(1), ENSG00000151366(1), ENSG00000155011(1), ENSG00000156049(1), ENSG00000156687(1), ENSG00000159210(1), ENSG00000161835(1), ENSG00000163697(1), ENSG00000163827(1), ENSG00000164220(1), ENSG00000164418(1), ENSG00000165959(1), ENSG00000170365(1), ENSG00000170855(1), ENSG00000171421(1), ENSG00000171843(1), ENSG00000174502(1), ENSG00000176177(1), ENSG00000176231(1), ENSG00000176244(1), ENSG00000180739(1), ENSG00000181029(1), ENSG00000182253(1), ENSG00000182752(1), ENSG00000184270(1), ENSG00000197562(1), ENSG00000213931(1), ENSG00000082458(1), ENSG00000099284(1), ENSG00000100348(1), ENSG00000109471(1), ENSG00000111725(1), ENSG00000112576(1), ENSG00000116539(1), ENSG00000118156(1), ENSG00000119684(1), ENSG00000125538(1), ENSG00000126012(1), ENSG00000128573(1), ENSG00000128908(1), ENSG00000130413(1), ENSG00000132964(1), ENSG00000136518(1), ENSG00000137285(1), ENSG00000139445(1), ENSG00000140465(1), ENSG00000143479(1), ENSG00000143761(1), ENSG00000144852(1), ENSG00000146006(1), ENSG00000146535(1), ENSG00000149923(1), ENSG00000158079(1), ENSG00000163577(1), ENSG00000166226(1), ENSG00000168280(1), ENSG00000170684(1), ENSG00000171956(1), ENSG00000172936(1), ENSG00000174963(1), ENSG00000183486(1), ENSG00000187144(1), ENSG00000197054(1), ENSG00000197561(1), ENSG00000198093(1), ENSG00000198742(1), ENSG00000204388(1), ENSG00000222014(1), ENSG00000261459(1), ENSG00000267001(1), ENSG00000023892(1), ENSG00000095203(1), ENSG00000101246(1), ENSG00000103042(1), ENSG00000104055(1), ENSG00000105784(1), ENSG00000106178(1), ENSG00000106609(1), ENSG00000120685(1), ENSG00000124116(1), ENSG00000129422(1), ENSG00000130783(1), ENSG00000132823(1), ENSG00000133030(1), ENSG00000133131(1), ENSG00000134207(1), ENSG00000134551(1), ENSG00000137441(1), ENSG00000140478(1), ENSG00000140479(1), ENSG00000140545(1), ENSG00000142511(1), ENSG00000144229(1), ENSG00000148814(1), ENSG00000149150(1), ENSG00000150201(1), ENSG00000152154(1), ENSG00000155066(1), ENSG00000158423(1), ENSG00000162062(1), ENSG00000162399(1), ENSG00000164674(1), ENSG00000165985(1), ENSG00000166926(1), ENSG00000168675(1), ENSG00000168903(1), ENSG00000168967(1), ENSG00000171695(1), ENSG00000172986(1), ENSG00000173269(1), ENSG00000173548(1), ENSG00000173597(1), ENSG00000175183(1), ENSG00000175967(1), ENSG00000177994(1), ENSG00000178457(1), ENSG00000179002(1), ENSG00000183742(1), ENSG00000185105(1), ENSG00000185955(1), ENSG00000186481(1), ENSG00000189127(1), ENSG00000196091(1), ENSG00000198685(1), ENSG00000204511(1), ENSG00000214575(1), ENSG00000226887(1), ENSG00000227268(1), ENSG00000241690(1), ENSG00000251537(1), ENSG00000253117(1), ENSG00000261794(1), ENSG00000265107(1), ENSG00000269405(1), ENSG00000269476(1), ENSG00000273590(1), ENSG00000278023(1), ENSG00000125910(1), ENSG00000136147(1), ENSG00000137474(1), ENSG00000142453(1), ENSG00000155849(1), ENSG00000156587(1), ENSG00000137203(1), ENSG00000159110(1), ENSG00000162496(1), ENSG00000166920(1), ENSG00000186431(1), ENSG00000120053(1), ENSG00000134627(1), ENSG00000138495(1), ENSG00000142634(1), ENSG00000147180(1), ENSG00000204618(1), ENSG00000269026(1), ENSG00000075426(1), ENSG00000149269(1), ENSG00000198739(1), ENSG00000013392(1), ENSG00000118922(1), ENSG00000121957(1), ENSG00000172350(1), ENSG00000274267(1)

5.4 Best C-index test in all runs

Best Elastic Net model (C-Index test)

[INFO] Coefs. list

[1] “ADAMDEC1, ADGRG5, ANG, ARMH1, B2M, CALHM1, CCL8, CIITA, CRIP1, CXCL9, ETV3L, GBP1, GBP2, GBP4, GJA10, HAPLN3, HLA-DQA1, HLA-DQB1, HOXB6, IFITM1, IL21R, KIR2DL4, KLRD1, MAP3K7CL, MEI1, MZB1, NLRP6, OR2M4, PATL2, PIM2, PLA2G2D, PSME2, RNF213, SLC25A52, SLC38A11, SULT1E1, TNFRSF4, TRIM69, ZBP1, ZNF667, ZRSR2”

Test set

Full set

Best Hub model (C-Index test)

[INFO] Coefs. list

[1] “ACTL7B, ACTL8, ACTR1B, ALB, CAD, CD8A, CDK2, CDK5, CTNNB1, EGFR, ESR1, FAU, GAPDH, HSP90AA1, ICAM1, IMPDH2, INSR, ISG15, KIT, LCK, LRRK2, MAPK1, MAPK14, MAPK3, MYH14, OAS1, OASL, PIM2, PPP3CC, PRKCG, RAB2B, RASD2, RHOA, RHOBTB2, RHOC, RHOJ, RRAS, TP53, TSPO, TUBB2A, UBC, UBD, UBL4A”

Test set

Full set

Best Orphan model (C-Index test)

[INFO] Coefs. list

[1] “AC114490.2, ADAMDEC1, ADGRG5, ARMH1, C11orf21, CALHM1, CAPS, CCDC8, CCL5, CCL8, CRIP1, CXorf58, CYBC1, ETV3L, FCRL6, GBA3, GBP5, GJA10, GRIPAP1, HAPLN3, HLA-DQA1, HSH2D, KIR2DL4, LCN9, LGALS17A, LINC00324, LINC00336, MAP3K7CL, MEI1, MZB1, NEURL3, NLRP6, PATL2, PLA2G2D, REC8, RNASE4, SLC25A52, SLC38A11, SLC66A1L, TIGIT, ZNF320, ZNF730”

Test set

Full set

5.5 Best Log-rank test in all runs

Best Elastic net (Log-rank test)

[INFO] Coefs. list

[1] “AACS, AC005520.1, ACTL8, ACY3, AIP, AL136295.1, ANG, APH1B, ASZ1, ATP13A4, B2M, BPY2B, C1orf185, C1QTNF8, C3orf49, CA11, CALHM1, CCL5, CCL8, CCNF, CD274, CD74, CDIP1, CNGA1, CPLX3, CRIP1, CTRB1, CXCL11, CXCL9, CXorf58, CYP26C1, EARS2, FANCE, FERD3L, FERMT3, FOLR1, FZD5, GBA3, GBP2, GJA10, GLIPR1L1, GLIS3, GRIPAP1, HAPLN3, HLA-B, HLA-DOB, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB5, HLA-F, HORMAD2, HPDL, HSFY2, IFFO1, IFITM1, IL18BP, IRF1, ISCU, ISL1, JPT2, KCNJ15, KCNMB1, KIR2DL4, KRT19, LCN9, LINC00324, LINC00336, MAGEB2, MAP3K7CL, MDGA1, MID1IP1, MIR99AHG, MROH2A, NIPAL1, NLRC5, NLRP6, NOTCH3, NTNG2, NYAP2, OR3A1, PAQR7, PARP8, PGGHG, PHF21B, PKIG, PPIAL4G, PPP1R12C, PPP3CC, PRM2, PSME2, RAB2B, REC8, RTL10, S100G, SCAMP5, SCNN1G, SLA2, SLC25A52, SLC34A2, SLC38A11, SLC7A2, SSTR2, SYDE2, SYT14, TARM1, TICRR, TMPRSS7, TRIM69, TTC39A, UNC13A, UTS2, WDR77, ZBP1, ZNF197, ZNF492, ZNF69, ZNF724, ZNF730, ZNF844, ZRSR2”

Test set

Full set

Best Hub model (Log-rank test)

[INFO] Coefs. list

[1] “ACTL6B, ACTL7B, ACTL8, ACTR1B, ALB, CD8A, CDK2, CDK3, CDK4, CIB4, DECR1, EGFR, EPHB1, ESR1, FAU, FGF2, GAPDH, GART, HSP90AA1, IMPDH2, INSR, KIT, LRRK2, MAPK1, MAPK14, MET, MYH14, OAS1, OAS2, OASL, PPP3CC, RAB25, RAC3, RAD51D, RHOJ, RHOV, TP53, TSPO, TUBA1C, TUBB2A, UBC, UBD, UBL4A, UBL4B, UMPS, ZFAND4”

Test set

Full set

Best Orphan model (Log-rank test)

[INFO] Coefs. list

[1] “ACY3, ADGRG5, BPY2B, BTN3A3, CCL5, CCL8, CRIP1, EARS2, FANCE, FERD3L, GBP5, GJA10, GRIPAP1, HAPLN3, HCP5, HLA-DOB, HLA-DPA1, HLA-DQA1, HLA-F, HPDL, HSH2D, IFITM1, IRF1-AS1, JPT2, KIR2DL4, LGALS17A, LINC00324, LINC00336, MAP3K7CL, NKG7, NLRC5, NLRP6, NYAP2, PARP8, REC8, RTL10, RUFY4, SLA2, SLC25A52, SLC38A11, TARM1, TICRR, TTC39A, ZNF730”

Test set

Full set

NULL

6 Parameters for the report

## [INFO]          balanced.sets: TRUE
## [INFO]        calc.params.old: FALSE
## [INFO]           coding.genes: TRUE
## [INFO]     degree.correlation: pearson
## [INFO]          degree.cutoff:       0.000
## [INFO]            degree.type: string
## [INFO]      degree.unweighted: TRUE
## [INFO]      handle.duplicates: keep_first
## [INFO]                   log2: TRUE
## [INFO]                n.cores:      14.000
## [INFO]          normalization: center
## [INFO]                 ntimes:    5000.000
## [INFO]                project: skcm.data.2018.09.11
## [INFO]                   seed:    1985.000
## [INFO]                 subset: Inf
## [INFO]   subtract.surv.column: days_to_submitted_specimen_dx
## [INFO]            target.vars: list(alpha = 0.1, vars = 116), list(alpha = 0.1, vars = 41), list(alpha = 0.1, vars = 111)
## [INFO]                 tissue: metastatic
## [INFO]                  train:       0.800